AffySNPCNVPDInfoPkgSeed2-class package:pdInfoBuilder R Documentation

_C_l_a_s_s "_A_f_f_y_S_N_P_C_N_V_P_D_I_n_f_o_P_k_g_S_e_e_d_2"

_D_e_s_c_r_i_p_t_i_o_n:

     A generic annotation package builder for Affymetrix SNP/CNV
     arrays. This is a simplified version of the annotation package and
     'crlmm' will *NOT* work for them.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form
     'new("AffySNPCNVPDInfoPkgSeed2", csvAnnoFileCnv, csvSeqFileCnv,
     ...)'.

_S_l_o_t_s:


     '_c_d_f_F_i_l_e': Path to the CDF file for this.

     '_c_s_v_A_n_n_o_F_i_l_e': Path to the Affymetrix CSV annotation for the SNP
          probes.

     '_c_s_v_S_e_q_F_i_l_e': Path to the (SNP) probe sequence file.

     '_c_s_v_A_n_n_o_F_i_l_e_C_n_v': Path to the Affymetrix CSV annotation for the
          CNV probes.

     '_c_s_v_S_e_q_F_i_l_e_C_n_v': Path to the (CNV) probe sequence file.

     '_c_h_i_p_N_a_m_e': Name of the chip or platform

     '_m_a_n_u_f_a_c_t_u_r_e_r': chip/platform manufacturer

     '_u_r_l': chip URL

     '_g_e_n_o_m_e_b_u_i_l_d': The genome build this platform is based upon.

     '_o_r_g_a_n_i_s_m': organism for chip. 

     '_s_p_e_c_i_e_s': species for chip.   

     '_v_e_r_s_i_o_n': A character vector giving the version number of the
          package.

     '_l_i_c_e_n_s_e': The license of the package

     '_a_u_t_h_o_r': Author of the package

     '_e_m_a_i_l': An email address to use in the Maintainer field

     '_b_i_o_c_V_i_e_w_s': Character data for the biocViews field of the
          DESCRIPTION file

_M_e_t_h_o_d_s:


     _c_h_i_p_N_a_m_e 'signature(object = "AffySNPCNVPDInfoPkgSeed2")': ... 

     _m_a_k_e_P_d_I_n_f_o_P_a_c_k_a_g_e 'signature(object =
          "AffySNPCNVPDInfoPkgSeed2")': ... 

_N_o_t_e:

     This is a simplified annotation package. CRLMM won't work for
     these objects.

     The user may need to rename the columns or even add column names
     to the annotation and sequence files. In case problems are found,
     column names are suggested.

_A_u_t_h_o_r(_s):

     Benilton Carvalho

_E_x_a_m_p_l_e_s:

     showClass("AffySNPCNVPDInfoPkgSeed2")

